FMO DATABASE

FMODB ID: 22YGR

Calculation Name: 1F39-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1F39

Chain ID: A

ChEMBL ID:
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UniProt ID: P03034

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-693123.685906
FMO2-HF: Nuclear repulsion	653933.33324
FMO2-HF: Total energy	-39190.352666
FMO2-MP2: Total energy	-39301.580968

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:136:ALA)

Summations of interaction energy for fragment #1(A:136:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-6.265	-1.463	3.532	-3.56	-4.776	-0.022

Interaction energy analysis for fragmet #1(A:136:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.040

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	138	ALA	0	-0.028	-0.023	3.742	-1.598	-0.326	-0.013	-0.664	-0.596	0.002
4	A	139	SER	0	-0.026	-0.047	6.330	0.357	0.357	0.000	0.000	0.000	0.000
5	A	140	ALA	0	-0.063	-0.024	2.785	0.046	0.480	0.269	-0.202	-0.502	-0.001
6	A	141	PHE	0	-0.036	-0.014	4.727	0.013	0.023	-0.001	-0.004	-0.005	0.000
7	A	142	TRP	0	-0.003	-0.007	6.665	0.199	0.199	0.000	0.000	0.000	0.000
8	A	143	LEU	0	-0.029	-0.009	9.072	0.001	0.001	0.000	0.000	0.000	0.000
9	A	144	GLU	-1	-0.884	-0.946	12.470	-0.074	-0.074	0.000	0.000	0.000	0.000
10	A	145	VAL	0	-0.118	-0.057	15.231	0.016	0.016	0.000	0.000	0.000	0.000
11	A	146	GLU	-1	-0.853	-0.911	17.345	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	147	GLY	0	-0.060	-0.027	20.805	0.013	0.013	0.000	0.000	0.000	0.000
13	A	148	ASN	0	0.023	-0.011	22.629	0.003	0.003	0.000	0.000	0.000	0.000
14	A	149	SER	0	-0.028	-0.008	22.148	0.013	0.013	0.000	0.000	0.000	0.000
15	A	150	MET	0	0.013	0.037	17.435	0.010	0.010	0.000	0.000	0.000	0.000
16	A	151	THR	0	-0.001	0.016	20.477	0.005	0.005	0.000	0.000	0.000	0.000
17	A	152	ALA	0	-0.003	-0.008	22.567	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	153	PRO	0	0.001	0.000	24.272	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	154	THR	0	0.040	0.010	26.947	0.006	0.006	0.000	0.000	0.000	0.000
20	A	155	GLY	0	-0.004	0.005	27.211	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	156	SER	0	-0.062	-0.021	25.195	0.008	0.008	0.000	0.000	0.000	0.000
22	A	157	LYS	1	0.942	0.989	20.438	-0.167	-0.167	0.000	0.000	0.000	0.000
23	A	158	PRO	0	-0.015	-0.028	16.917	0.004	0.004	0.000	0.000	0.000	0.000
24	A	159	SER	0	0.004	-0.011	18.516	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	160	PHE	0	0.004	-0.001	13.602	0.010	0.010	0.000	0.000	0.000	0.000
26	A	161	PRO	0	-0.033	-0.021	18.128	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	162	ASP	-1	-0.831	-0.910	19.309	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	163	GLY	0	0.054	0.032	19.697	0.000	0.000	0.000	0.000	0.000	0.000
29	A	164	MET	0	-0.114	-0.034	14.660	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	165	LEU	0	0.050	0.037	11.895	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	166	ILE	0	-0.041	-0.030	10.290	0.047	0.047	0.000	0.000	0.000	0.000
32	A	167	LEU	0	-0.014	-0.006	2.778	-0.489	-0.110	0.245	-0.144	-0.480	0.000
33	A	168	VAL	0	0.012	-0.002	7.078	0.283	0.283	0.000	0.000	0.000	0.000
34	A	169	ASP	-1	-0.716	-0.841	2.455	-1.915	-0.299	2.058	-1.987	-1.687	-0.022
35	A	170	PRO	0	0.001	-0.017	5.387	0.313	0.336	-0.001	-0.001	-0.020	0.000
36	A	171	GLU	-1	-0.913	-0.918	6.003	-0.386	-0.386	0.000	0.000	0.000	0.000
37	A	172	GLN	0	-0.106	-0.039	2.712	-1.228	-0.648	0.131	-0.256	-0.456	0.000
38	A	173	ALA	0	0.015	0.005	7.389	-0.241	-0.241	0.000	0.000	0.000	0.000
39	A	174	VAL	0	-0.023	-0.012	10.617	0.124	0.124	0.000	0.000	0.000	0.000
40	A	175	GLU	-1	-0.938	-0.965	12.716	0.405	0.405	0.000	0.000	0.000	0.000
41	A	176	PRO	0	-0.039	-0.041	15.522	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	177	GLY	0	-0.075	-0.044	17.872	0.012	0.012	0.000	0.000	0.000	0.000
43	A	178	ASP	-1	-0.837	-0.909	12.415	0.723	0.723	0.000	0.000	0.000	0.000
44	A	179	PHE	0	-0.022	-0.029	12.695	-0.094	-0.094	0.000	0.000	0.000	0.000
45	A	180	CYS	0	-0.034	-0.011	11.896	0.075	0.075	0.000	0.000	0.000	0.000
46	A	181	ILE	0	0.056	0.040	12.197	-0.049	-0.049	0.000	0.000	0.000	0.000
47	A	182	ALA	0	-0.006	-0.012	14.143	0.021	0.021	0.000	0.000	0.000	0.000
48	A	183	ARG	1	0.846	0.920	17.032	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	184	LEU	0	-0.005	-0.014	19.451	0.015	0.015	0.000	0.000	0.000	0.000
50	A	185	GLY	0	0.042	0.013	23.081	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	186	GLY	0	-0.022	0.002	26.394	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	187	ASP	-1	-0.881	-0.948	22.831	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	188	GLU	-1	-0.888	-0.925	21.833	0.013	0.013	0.000	0.000	0.000	0.000
54	A	189	PHE	0	0.010	-0.015	14.559	0.017	0.017	0.000	0.000	0.000	0.000
55	A	190	THR	0	-0.003	0.010	18.293	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	191	PHE	0	0.060	0.028	13.868	0.015	0.015	0.000	0.000	0.000	0.000
57	A	192	LYS	1	0.857	0.901	16.582	-0.110	-0.110	0.000	0.000	0.000	0.000
58	A	193	LYS	1	0.952	0.995	16.362	-0.220	-0.220	0.000	0.000	0.000	0.000
59	A	194	LEU	0	0.027	0.040	16.575	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	195	ILE	0	-0.004	-0.006	18.435	0.031	0.031	0.000	0.000	0.000	0.000
61	A	196	ARG	1	0.941	0.952	21.408	-0.230	-0.230	0.000	0.000	0.000	0.000
62	A	197	ASP	-1	-0.901	-0.939	24.065	0.137	0.137	0.000	0.000	0.000	0.000
63	A	198	SER	0	0.003	-0.001	27.739	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	199	GLY	0	-0.048	-0.026	27.967	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	200	GLN	0	-0.028	-0.006	27.390	0.000	0.000	0.000	0.000	0.000	0.000
66	A	201	VAL	0	0.036	0.021	21.031	0.011	0.011	0.000	0.000	0.000	0.000
67	A	202	PHE	0	-0.012	-0.005	23.106	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	203	LEU	0	0.003	0.007	18.929	0.024	0.024	0.000	0.000	0.000	0.000
69	A	204	GLN	0	-0.013	-0.034	21.184	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	205	PRO	0	0.023	0.014	21.134	0.017	0.017	0.000	0.000	0.000	0.000
71	A	206	LEU	0	-0.013	-0.023	18.685	0.005	0.005	0.000	0.000	0.000	0.000
72	A	207	ASN	0	0.000	0.012	22.937	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	208	PRO	0	0.003	-0.027	25.901	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	209	GLN	0	-0.035	-0.008	29.046	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	210	TYR	0	-0.027	-0.007	26.632	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	211	PRO	0	-0.002	0.005	28.423	0.006	0.006	0.000	0.000	0.000	0.000
77	A	212	MET	0	0.006	-0.001	26.015	0.008	0.008	0.000	0.000	0.000	0.000
78	A	213	ILE	0	-0.005	-0.007	24.192	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	214	PRO	0	-0.010	0.003	24.714	0.014	0.014	0.000	0.000	0.000	0.000
80	A	215	CYS	0	-0.034	-0.005	21.150	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	216	ASN	0	0.001	-0.020	23.843	0.015	0.015	0.000	0.000	0.000	0.000
82	A	217	GLU	-1	-0.905	-0.962	24.278	0.080	0.080	0.000	0.000	0.000	0.000
83	A	218	SER	0	-0.029	-0.003	25.001	0.001	0.001	0.000	0.000	0.000	0.000
84	A	219	CYS	0	-0.082	-0.020	21.068	0.002	0.002	0.000	0.000	0.000	0.000
85	A	220	SER	0	0.031	0.017	18.741	0.006	0.006	0.000	0.000	0.000	0.000
86	A	221	VAL	0	0.032	-0.001	13.065	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	222	VAL	0	-0.038	-0.009	12.002	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	223	GLY	0	0.055	0.009	9.438	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	224	LYS	1	0.939	0.992	7.442	-1.454	-1.454	0.000	0.000	0.000	0.000
90	A	225	VAL	0	-0.038	-0.006	7.419	0.017	0.017	0.000	0.000	0.000	0.000
91	A	226	ILE	0	-0.047	-0.039	2.650	-0.463	0.025	0.844	-0.302	-1.030	-0.001
92	A	227	ALA	0	-0.022	-0.009	5.708	-0.051	-0.051	0.000	0.000	0.000	0.000
93	A	228	SER	0	-0.025	-0.025	7.540	-0.034	-0.034	0.000	0.000	0.000	0.000
94	A	229	GLN	0	-0.006	0.008	9.932	0.026	0.026	0.000	0.000	0.000	0.000
95	A	230	TRP	0	0.027	0.010	12.895	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	231	PRO	0	0.046	0.032	15.325	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	232	GLU	-1	-0.898	-0.940	15.645	-0.202	-0.202	0.000	0.000	0.000	0.000
98	A	233	GLU	-1	-0.865	-0.958	17.844	-0.133	-0.133	0.000	0.000	0.000	0.000
99	A	234	THR	0	-0.088	-0.043	19.048	0.015	0.015	0.000	0.000	0.000	0.000
100	A	235	PHE	0	-0.093	-0.052	18.162	0.015	0.015	0.000	0.000	0.000	0.000
101	A	236	GLY	0	-0.054	-0.007	23.017	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:136:ALA)